Objective To screen transgenic Houttuynia cordata Thunb. and to analyze the stability of exogenous genes initially. Methods Kanamycin was smeared to the surface of the ]eaves to screen the transgenic plants containing the npt Ⅱ gene. And then PCR detection of the npt Ⅱ gene and target gene CN (cecropin B/NP-1 )was carried out in kanamycin-resistance plant. Results The results of kanamycin-smearing screening method showed that the optimal kanamycin concentration was 5000 mg/L and the optimal observation time was day 1 to day 4. The result of PCR analysis showed that the expression ratio of resistant gene npt Ⅱ was 96% in the resistant plants, and the expression ratio of target gene CN was 37%. Conclusion A method for quickly screening transgenic Houttuynia cordata Thunb. has been established. The stability of target gene in the transgenic plant is inferior to the selecting maker gene.